JANEWAY: Computer, display Fair Haven character Michael Sullivan. Adjust his parameters to the following specifications. Give him the education of a nineteenth century third year student at Trinity College.
COMPUTER: Modification complete.
JANEWAY: Now, access the character's interactive subroutines. Make him more provocative.
COMPUTER: Specify.
JANEWAY: Give him a more complicated personality.
COMPUTER: Specify.
JANEWAY: More outspoken, more confident, not so reserved, and make him more curious about the world around him.
COMPUTER: Modification complete.
JANEWAY: Good. Now, increase the character's height by three centimetres. Remove the facial hair. No, no, I don't like that. Put some back. About two days' growth. Better. Oh, one more thing. Access his interpersonal subroutines, familial characters. Delete the wife.

For me, it's the opening scene of Voyager's "Macrocosm" where Neelix is negotiating with the Tak-Tak. Whenever I watch that scene, my mind is torn between thinking... "What in the..." and cringing. I know it's a form of communication, but it is bizarre.

Oh, and those C/7 scenes in "Endgame". Chakotay's "I want to make sure it's in transporter range of you" is like being forced to swallow a bucket of sugar. It's just too cheesy and unrealistic for my tastes.

In NEM: Wesley back in uniform with no explanation, Worf back in uniform with no explanation, the driving scene, Troi having to use Worf's hand to target weapons (she could have done it just as easily herself), B-4 becoming Data 2.0.

Emotion-chip Data in Generations, though? Seriously, seriously annoying. Holodoc and Neelix on VOY were sometimes annoying too, but there you at least got the idea that it was intended to be so; with Data, it felt more like a misbegotten idea gone horribly wrong. (Or Spiner given free rein - one of those.)

For me, it goes to Rom hollering WAAAAAAAAAAAAAAIT in the DS9 season 5 episode Doctor Bashir, I Presume.
That scene just gets on my last good nerve.
Okay, now I wanna hear from you what scene from which Trek series gets on your last good nerve.

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Haha, I remember that scene.

There were many scenes with Rom in DS9 & Troi in TNG that were epically unbearable....